论文：
1. Jin, X., Huang, G., Luo, Z., Hu, Y., & Liu, D*. 2022. Oregano (Origanum vulgare L.) Essential Oil Feed Supplement Protected Broilers Chickens against Clostridium perfringens Induced Necrotic Enteritis. Agriculture-Basel, 12(1): 18.
2. Feng, Y., Wang, Y., Zhu, B., Gao, G. F., Guo, Y., & Hu, Y*. 2021. Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes. Commun Biol, 4: 1305.
3. Hu, X., Zhou, X., Yin, T., Chen, K., Hu, Y., Zhu, B., & Mi, K. 2021. The Mycobacterial DNA Methyltransferase HsdM Decreases Intrinsic Isoniazid Susceptibility. Antibiotics, 10(11): 1323.
4. Lyu, N., Feng, Y., Pan, Y., Huang, H., Liu, Y., Xue, C., Zhu, B., & Hu, Y.* 2021. Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China. Front Microbiol, 12:636332.
5. Pan, Y., Fang, Y., Feng, Y., Lyu, N., Chen, L., Li, J., Xu, X., Zhu, B., & Hu, Y*. 2021. Discovery of mcr-3.1 gene carried by a prophage located in a conjugative IncA/C2 plasmid from a Salmonella Choleraesuis clinical isolate. J Infect, 82(3):414-451.
6. Chu, H., Hu, Y., Zhang, B., Sun, Z., & Zhu, B*. 2021. DNA Methyltransferase HsdM Induce Drug Resistance on Mycobacterium tuberculosis via Multiple Effects. Antibiotics (Basel), 10(12):1544.
7. Pan, Y., Fang, Y., Song, X., Lyu, N., Chen, L., Feng, Y., Xu, X., Zhu, B., & Hu, Y*. 2021. Co-occurrence of mcr-9, extended spectrum beta-lactamase (ESBL) and AmpC genes ina conjugative IncHI2A plasmid from a multidrug-resistant clinical isolate of Salmonella diarizonae. J Infect, 82(4):84-123.
8. Wang, Y., Li, Z., Lyu, N., Ma, S., Liu, F., Hu, Y., Gao, G. F., & Zhu, B. 2021. Comparative genomic analysis of mobile colistin resistance gene mcr-9 in Salmonella enterica. J Infect, 82(4):e15-e17.
9. Wang, Y., Lyu, N., Liu, F., Liu, W. J., Bi, Y., Zhang, Z., Ma, S., Cao, J., Song, X., Wang, A., Zhang, G., Hu, Y.*, Zhu, B.*, & Gao, G. F.* 2021. More diversified antibiotic resistance genes in chickens and workers of the live poultry markets. Environ Int, 153: 106534. (IF5=10.720)
10. Cao, J.#, Hu, Y.#, Liu, F.#, Wang, Y., Bi, Y., Lv, N., Li, J., Zhu, B., & Gao, G. F. 2020. Metagenomic analysis reveals the microbiome and resistome in migratory birds. Microbiome, 8(1): 26. (IF5=15.677)
11. Cao, L., Chen, H., Wang, Q., Li, B., Hu, Y., Zhao, C., Hu, Y.*, & Yin, Y*. 2020. Literature-Based Phenotype Survey and In Silico Genotype Investigation of Antibiotic Resistance in the Genus Bifidobacterium. Curr Microbiol, 77: 4104–4113.
12. Feng, Y., Fan, X., Zhu, L., Yang, X., Liu, Y., Gao, S., Jin, X., Liu, D., Ding, J., Guo, Y., & Hu, Y.* 2020. Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens. Microb Genom, 6(10): mgen000441.
13. Huang, C., Ming, D., Wang, W., Wang, Z., Hu, Y., Ma, X., & Wang, F. 2020. Pyrroloquinoline Quinone Alleviates Jejunal Mucosal Barrier Function Damage and Regulates Colonic Microbiota in Piglets Challenged With Enterotoxigenic Escherichia coli. Front Microbiol, 11:1754.
14. Wang, Y., Hu, Y.*, & Gao, G. F. 2020. Combining metagenomics and metatranscriptomics to study human, animal and environmental resistomes. Medicine in Microecology, 3: 100014.
15. Tang, D., Li, Z., Mahmood, T., Liu, D., Hu, Y., & Guo, Y. 2020. The association between microbial community and ileal gene expression on intestinal wall thickness alterations in chickens. Poult Sci, 99(4): 1847-1861.
16. Wang, Y.#, Hu, Y.#, Liu, F., Cao, J., Lv, N., Zhu, B., Zhang, G., & Gao, G. F. 2020. Integrated metagenomic and metatranscriptomic profiling reveals differentially expressed resistomes in human, chicken, and pig gut microbiomes. Environ Int, 138: 105649. (IF5=10.720)
17. Wang, Y.#, Hu, Y.#, Cao, J., Bi, Y., Lv, N., Liu, F., Liang, S., Shi, Y., Jiao, X., Gao, G. F., & Zhu, B. 2019. Antibiotic resistance gene reservoir in live poultry markets. J Infect, 78(6):445-453.
18. Hu, Y., Feng, Y., Wu, J., Liu, F., Zhang, Z., Hao, Y., Liang, S., Li, B., Li, J., Lv, N., Xu, Y.*, Zhu, B.*, & Sun, Z*. 2019. The Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients. Front Cell Infect Microbiol, 9:90.
19. Wang, Y., Liu, F., Hu, Y., Zhang, G., Zhu, B., & Gao, G. F. 2019. Detection of mobile colistin resistance gene mcr-9 in carbapenem-resistant Klebsiella pneumoniae strains of human origin in Europe. J Infect, 80(5):578-606.
20. Song, X., Zhong, L., Lyu, N., Liu, F., Li, B., Hao, Y., Xue, Y., Li, J., Feng, Y., Ma, Y., Hu, Y.*, & Zhu, B.* 2019. Inulin Can Alleviate Metabolism Disorders in ob/ob Mice by Partially Restoring Leptin-related Pathways Mediated by Gut Microbiota. Genomics Proteomics Bioinformatics, 17(1):64-75. (IF5=11.120)
21. Lu, X., Zeng, M., Xu, J., Zhou, H., Gu, B., Li, Z., Jin, H., Wang, X., Zhang, W., Hu, Y., Xiao, W., Zhu, B., Xu, X., & Kan, B. 2019. Epidemiologic and genomic insights on mcr-1-harbouring Salmonella from diarrhoeal outpatients in Shanghai, China, 2006-2016. EBioMedicine, 42: 133-144.
22. Xu, Y., Liu, F., Chen, S., Wu, J., Hu, Y., Zhu, B., & Sun, Z. 2018. In vivo evolution of drug-resistant Mycobacterium tuberculosis in patients during long-term treatment. BMC Genomics, 19(1): 640.
23. Liu, W. J.#, Zou, R.#, Hu, Y.#, Zhao, M., Quan, C., Tan, S., Luo, K., Yuan, J., Zheng, H., Liu, J., Liu, M., Bi, Y., Yan, J., Zhu, B., Wang, D., Wu, G., Liu, L., Yuen, K. Y., Gao, G. F., & Liu, Y. 2018. Clinical, immunological and bacteriological characteristics of H7N9 patients nosocomially co-infected by Acinetobacter Baumannii: a case control study. BMC Infect Dis, 18(1): 664.
24. Alkasir, R., Ma, Y., Liu, F., Li, J., Lv, N., Xue, Y., Hu, Y.*, & Zhu, B*. 2018. Characterization and Transcriptome Analysis of Acinetobacter baumannii Persister Cells. Microb Drug Resist, 24(10): 1466-1474.
25. Zhang, C., Feng, Y., Liu, F., Jiang, H., Qu, Z., Lei, M., Wang, J., Zhang, B., Hu, Y., Ding, J., & Zhu, B. 2017. A Phage-Like IncY Plasmid Carrying the mcr-1 Gene in Escherichia coli from a Pig Farm in China. Antimicrob Agents Chemother, 61(3): e02035-16.
26. Lu, X.#, Hu, Y.#, Luo, M., Zhou, H., Wang, X., Du, Y., Li, Z., Xu, J., Zhu, B., Xu, X., & Kan, B. 2017. MCR-1.6, a New MCR Variant Carried by an IncP Plasmid in a Colistin-Resistant Salmonella enterica Serovar Typhimurium Isolate from a Healthy Individual. Antimicrob Agents Chemother, 61(5): e02632-16.
27. Hu, Y.*, Gao, G. F., & Zhu, B*. 2017. The antibiotic resistome: gene flow in environments, animals and human beings. Front Med, 11(2): 161-168.
28. Hu, Y., & Zhu, B. 2016. The Human Gut Antibiotic Resistome in the Metagenomic Era: Progress and Perspectives. Infect Dis Transl Med, 2(1): 41-47.
29. Hu, Y., Yang, X., Li, J., Lv, N., Liu, F., Wu, J., Lin, I. Y., Wu, N., Weimer, B. C., Gao, G. F., Liu, Y., & Zhu, B. 2016. The Bacterial Mobile Resistome Transfer Network Connecting the Animal and Human Microbiomes. Appl Environ Microbiol, 82(22): 6672-6681.
30. Hu, Y., Liu, F., Lin, I. Y., Gao, G. F., & Zhu, B. 2016. Dissemination of the mcr-1 colistin resistance gene. Lancet Infect Dis, 16(2): 146-147. (IF5=25.023)
31. Gao, R.#, Hu, Y.#, Li, Z.#, Sun, J.#, Wang, Q., Lin, J., Ye, H., Liu, F., Srinivas, S., Li, D., Zhu, B., Liu, Y. H., Tian, G. B., & Feng, Y. 2016. Dissemination and Mechanism for the MCR-1 Colistin Resistance. PLoS Pathog, 12(11): e1005957.
32. Yang, X., Liu, D., Lv, N., Zhao, F., Liu, F., Zou, J., Chen, Y., Xiao, X., Wu, J., Liu, P., Gao, J., Hu, Y., Shi, Y., Liu, J., Zhang, R., Chen, C., Ma, J., Gao, G. F., & Zhu, B. 2015. TCRklass: a new K-string-based algorithm for human and mouse TCR repertoire characterization. J Immunol, 194(1): 446-454.
33. Luan, C., Xie, L., Yang, X., Miao, H., Lv, N., Zhang, R., Xiao, X., Hu, Y., Liu, Y., Wu, N., Zhu, Y., & Zhu, B. 2015. Dysbiosis of fungal microbiota in the intestinal mucosa of patients with colorectal adenomas. Sci Rep, 5: 7980.
34. Liu, F., Yang, X., Wang, Z., Nicklasson, M., Qadri, F., Yi, Y., Zhu, Y., Lv, N., Li, J., Zhang, R., Guo, H., Zhu, B., Sjoling, A.*, & Hu, Y*. 2015. Draft genomes of four enterotoxigenic Escherichia coli (ETEC) clinical isolates from China and Bangladesh. Gut Pathog, 7: 10.
35. Li, X., Wu, J., Han, J., Hu, Y., & Mi, K. 2015. Distinct Responses of Mycobacterium smegmatis to Exposure to Low and High Levels of Hydrogen Peroxide. PLoS One, 10(7): e0134595.
36. Li, H., Liu, F., Zhang, Y., Wang, X., Zhao, C., Chen, H., Zhang, F., Zhu, B., Hu, Y.*, & Wang, H.* 2015. Evolution of carbapenem-resistant Acinetobacter baumannii revealed through whole-genome sequencing and comparative genomic analysis. Antimicrob Agents Chemother, 59(2): 1168-1176.
37. Hu, Y., Zhu, Y., Ma, Y., Liu, F., Lu, N., Yang, X., Luan, C., Yi, Y., & Zhu, B. 2015. Genomic insights into intrinsic and acquired drug resistance mechanisms in Achromobacter xylosoxidans. Antimicrob Agents Chemother, 59(2): 1152-1161.
38. Hu, Y.#, Liu, Y#., Li, J., Feng, Y., Lu, N., Zhu, B., & Xue, S. 2015. Structural and functional analysis of a low-temperature-active alkaline esterase from South China Sea marine sediment microbial metagenomic library. J Ind Microbiol Biotechnol, 42(11): 1449-1461.
39. Zhu, Y., Yi, Y., Liu, F., Lv, N., Yang, X., Li, J., Hu, Y.*, & Zhu, B*. 2014. Distribution and molecular profiling of class 1 integrons in MDR Acinetobacter baumannii isolates and whole genome-based analysis of antibiotic resistance mechanisms in a representative strain. Microbiol Res, 169(11): 811-816.
40. Yi, Y., Lu, N., Liu, F., Li, J., Zhang, R., Jia, L., Jing, H., Xia, H., Yang, Y., Zhu, B., Hu, Y.*, & Cui, Y*. 2014. Genome sequence and comparative analysis of a Vibrio cholerae O139 strain E306 isolated from a cholera case in China. Gut Pathog, 6(1): 3.
41. Lu, N.#, Hu, Y.#, Zhu, L.#, Yang, X., Yin, Y., Lei, F., Zhu, Y., Du, Q., Wang, X., Meng, Z., & Zhu, B. 2014. DNA microarray analysis reveals that antibiotic resistance-gene diversity in human gut microbiota is age related. Sci Rep, 4: 4302.
42. Liu, F., Zhu, Y., Yi, Y., Lu, N., Zhu, B.*, & Hu, Y*. 2014. Comparative genomic analysis of Acinetobacter baumannii clinical isolates reveals extensive genomic variation and diverse antibiotic resistance determinants. BMC Genomics, 15: 1163.
43. Liu, F.#, Hu, Y.#, Wang, Q., Li, H. M., Gao, G. F., Liu, C. H., & Zhu, B. 2014. Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates. BMC Genomics, 15: 469.
44. Li, X., Liu, F., Hu, Y., & Mi, K. 2014. Draft Genome Sequence of mc251, a Highly Hydrogen Peroxide-Resistant Mycobacterium smegmatis Mutant Strain. Genome Announc, 2(1): e00092-14.
45. Hu, Y., Yang, X., Lu, N., & Zhu, B. 2014. The abundance of antibiotic resistance genes in human guts has correlation to the consumption of antibiotics in animal. Gut Microbes, 5(2): 245-249. (IF5=12.117)
46. Wu, N., Yang, X., Zhang, R., Li, J., Xiao, X., Hu, Y., Chen, Y., Yang, F., Lu, N., Wang, Z., Luan, C., Liu, Y., Wang, B., Xiang, C., Wang, Y., Zhao, F., Gao, G. F., Wang, S., Li, L., Zhang, H., & Zhu, B. 2013. Dysbiosis signature of fecal microbiota in colorectal cancer patients. Microb Ecol, 66(2): 462-470.
47. Li, B.#, Hu, Y.#, Wang, Q.#, Yi, Y., Woo, P. C., Jing, H., Zhu, B., & Liu, C. H. 2013. Structural diversity of class 1 integrons and their associated gene cassettes in Klebsiella pneumoniae isolates from a hospital in China. PLoS One, 8(9): e75805.
48. Hu, Y.#, Yang, X.#, Qin, J., Lu, N., Cheng, G., Wu, N., Pan, Y., Li, J., Zhu, L., Wang, X., Meng, Z., Zhao, F., Liu, D., Ma, J., Qin, N., Xiang, C., Xiao, Y., Li, L., Yang, H., Wang, J., Yang, R., Gao, G. F., Wang, J., & Zhu, B. 2013. Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota. Nat Commun, 4: 2151. (IF5=15.805)
49. Cheng, G., Hu, Y., Lu, N., Li, J., Wang, Z., Chen, Q., & Zhu, B. 2013. Identification of a novel fosfomycin-resistant UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) from a soil metagenome. Biotechnol Lett, 35(2): 273-278.
50. Wu, N., Zhang, Y., Fu, J., Zhang, R., Feng, L., Hu, Y., Li, X., Lu, N., Zhao, X., Pan, Y., Li, J., Zhu, B., & Wan, K. 2012. Performance assessment of a novel two-step multiple displacement amplification-PCR assay for detection of Mycobacterium tuberculosis complex in sputum specimens. J Clin Microbiol, 50(4): 1443-1445.
51. Liu, C. H., Li, H. M., Lu, N., Wang, Q., Hu, Y. L., Yang, X., Hu, Y. F., Woo, P. C., Gao, G. F., & Zhu, B. 2012. Genomic sequence based scanning for drug resistance-associated mutations and evolutionary analysis of multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis. J Infect, 65(5): 412-422.
52. Hu, H.#, Hu, Y.#, Pan, Y., Liang, H., Wang, H., Wang, X., Hao, Q., Yang, X., Yang, X., Xiao, X., Luan, C., Yang, Y., Cui, Y., Yang, R., Gao, G. F., Song, Y., & Zhu, B. 2012. Novel plasmid and its variant harboring both a bla(NDM-1) gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii. Antimicrob Agents Chemother, 56(4): 1698-1702.
53. Cheng, G., Hu, Y., Yin, Y., Yang, X., Xiang, C., Wang, B., Chen, Y., Yang, F., Lei, F., Wu, N., Lu, N., Li, J., Chen, Q., Li, L., & Zhu, B. 2012. Functional screening of antibiotic resistance genes from human gut microbiota reveals a novel gene fusion. FEMS Microbiol Lett, 336(1): 11-16.
54. Pan, Y., Yang, X., Li, J., Zhang, R., Hu, Y., Zhou, Y., Wang, J., & Zhu, B. 2011. Genome sequence of the Spinosyns-producing bacterium Saccharopolyspora spinosa NRRL 18395. J Bacteriol, 193(12): 3150-3151.
55. Pan, Y., Yang, X., Duan, J., Lu, N., Leung, A. S., Tran, V., Hu, Y., Wu, N., Liu, D., Wang, Z., Yu, X., Chen, C., Zhang, Y., Wan, K., Liu, J., & Zhu, B. 2011. Whole-genome sequences of four Mycobacterium bovis BCG vaccine strains. J Bacteriol, 193(12): 3152-3153.
56. Hu, Y.#, Zhang, W.#, Liang, H., Liu, L., Peng, G., Pan, Y., Yang, X., Zheng, B., Gao, G. F., Zhu, B., & Hu, H. 2011. Whole-genome sequence of a multidrug-resistant clinical isolate of Acinetobacter lwoffii. J Bacteriol, 193(19): 5549-5550.
57. Fu, C.#, Hu, Y.#, Xie, F., Guo, H., Ashforth, E. J., Polyak, S. W., Zhu, B., & Zhang, L. 2011. Molecular cloning and characterization of a new cold-active esterase from a deep-sea metagenomic library. Appl Microbiol Biotechnol, 90(3): 961-970.
58. Zhao, W., Zhong, Y., Yuan, H., Wang, J., Zheng, H., Wang, Y., Cen, X., Xu, F., Bai, J., Han, X., Lu, G., Zhu, Y., Shao, Z., Yan, H., Li, C., Peng, N., Zhang, Z., Zhang, Y., Lin, W., Fan, Y., Qin, Z., Hu, Y., Zhu, B., Wang, S., Ding, X., & Zhao, G. P. 2010. Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism. Cell Res, 20(10): 1096-1108.
59. Hu, Y., Fu, C., Yin, Y., Cheng, G., Lei, F., Yang, X., Li, J., Ashforth, E. J., Zhang, L., & Zhu, B. 2010. Construction and preliminary analysis of a deep-sea sediment metagenomic fosmid library from Qiongdongnan Basin, South China Sea. Mar Biotechnol (NY), 12(6): 719-727.
60. Hu, Y., Fu, C., Huang, Y., Yin, Y., Cheng, G., Lei, F., Lu, N., Li, J., Ashforth, E. J., Zhang, L., & Zhu, B. 2010. Novel lipolytic genes from the microbial metagenomic library of the South China Sea marine sediment. FEMS Microbiol Ecol, 72(2): 228-237.
61. Angly, F. E., Willner, D., Prieto-Davo, A., Edwards, R. A., Schmieder, R., Vega-Thurber, R., Antonopoulos, D. A., Barott, K., Cottrell, M. T., Desnues, C., Dinsdale, E. A., Furlan, M., Haynes, M., Henn, M. R., Hu, Y., Kirchman, D. L., McDole, T., McPherson, J. D., Meyer, F., Miller, R. M., Mundt, E., Naviaux, R. K., Rodriguez-Mueller, B., Stevens, R., Wegley, L., Zhang, L., Zhu, B., & Rohwer, F. 2009. The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS Comput Biol, 5(12): e1000593.
62. 阿拉腾珠拉，胡永飞*。褐藻寡糖的制备方法及生物活性研究进展。生物工程学报，2022, 38(4): 1-14。
63. 胡永飞。微生物组学研究的“淘金时代”。微生物学报，2019, 9: 1631-1635。
64. 胡永飞，朱宝利。细菌耐药专刊序言。生物工程学报，2018, 8: 1201-1204。
65. 王亚楠，胡永飞*，朱宝利，焦新安，高福。养殖动物及其相关环境耐药组的研究进展。生物工程学报，2018，34(8): 1226-1233。（生物工程学报2020年度优秀论文奖）
66. 马亚男，朱玉莹，李维城，刘飞，律娜，李晶，朱宝利*，胡永飞*。鲍曼不动杆菌耐药持留菌的特征及Ⅱ型毒素-抗毒素系统的多样性。微生物学报，2015，55(7): 949-958.
67. 朱玉莹，易勇，杨犀，律娜，李晶，朱宝利*，胡永飞*。多重耐药铜绿假单胞菌中Ⅰ型整合子新结构的发现及其与耐药的相关性。微生物学报，2013, 53(9): 927-932。（微生物学报年度优秀学术论文）
68. 段嘉，程功，胡永飞，李晶，律娜，朱宝利。肠道微生物宏基因组文库构建及酯解酶基因筛选。中国农业大学学报，2013, 18(1): 10-15。
69. 张博，李铁民，杨智勇，胡永飞，李玉。谷氨酸棒杆菌H+-ATPase基因失活提高谷氨酸产生量。中国生物工程杂志, 2011, 31(1): 35-39。
70. 徐士庆，胡永飞，袁爱花，朱宝利。深海沉积物微生物元基因组文库来源的新的酯酶基因的克隆、表达及酶学性质。微生物学报，2010, 50(7): 891-896。
71. 胡永飞，李铁民，张博，杨志勇，李玉。抗噬菌体重组钝齿棒杆菌的生理稳定性。2010，30(6): 51-54。
72. 胡永飞，李铁民，杨智勇等。限制修饰系统cglI 赋予钝齿棒杆菌抗噬菌体功能活性。生物工程学报，2008, 24(5): 760-765。
73. 张博，杨智勇，胡永飞，杨柯，李玉，李铁民。噬菌体一指示菌模型检测固型板材抗病毒性能的方法研究。微生物学杂志，2008, 28(4): 27-29。
74. 郭树凡，朱春玉，李辉，胡永飞，李玉。磷细菌PB12菌株的选育及培养条件的研究。微生物学杂志，2007, 27(2): 49-52。
75. 胡永飞，李铁民。 基因工程技术在建立噬菌体抗性机制研究中的应用。微生物学杂志，2006, 26(6): 89-91。
76. 李铁民，胡永飞，冯倩妮，李玉，董占双，刘忠顺，罗恩杰。CglI基因在大肠杆菌中的功能活性分析。微生物学杂志，2006, 26(2): 41-44。
著作：
1. 耐药菌小史。中信出版社，2021年5月，ISBN：9787521730166，译著审校。
2. 传染性疾病与精准预防。上海交通大学出版社，2020年3月，ISBN：9787313204820，参编。
3. 细菌耐药危机下的挑战与对策——专家视角。人民卫生出版社，2019年8月，ISBN：978-7-117-28636-7，参编。
4. 肠道菌群与精准营养健康。中国科学技术出版社，2019年3月，ISBN：978-7-5046-7538-5/Q215，副主编。
5. 国家卫生和计划生育委员会“十二五”规划教材：医学微生态学。人民卫生出版社，出版日期2014年8月1日，ISBN：9787117190077，参编。